Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcgtctgaaaaaccgtctcctctacttttgatggctatcttgcaaaacactgagctgaggtattgcgattccttgttggcatgctgttggttggccctatgagagtagaatcttatttctgttacttaatattatgtgtagAGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGATATGTTGAGA
Basic information
species | Physcomitrella patens |
transcript | PP1S13_282V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S13_282V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtcgtctgaaaaaccgtctcctctacttttgatggctatcttgcaaaacactgagctgaggtattgcgattccttgttggcatgctgttggttggccctatgagagtagaatcttatttctgttacttaatattatgtgtagAGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGATATGTTGAGA
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---------------------------------------gtaagttccagtac-ctactttacctgagtgaaagtcatgactggt-taccctttcatagtttgatgataatt-attcaaattttt----ctttgcatc--gtccagGCTGCAGTTCTGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATAAAGTTTTGCCCAACCAAGGAGGAGATGGAGCTACTTAAG
upper sequence: PP1S13_282V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtcgtctgaaaaaccgtctcctctacttttgatggctatcttgcaaaacactgagctgaggtattgcgattccttgttggcatgctgttggttggccctatgagagtagaatcttatttctgttacttaatattatgtgtagAGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGATATGTTGAGA
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-----------------------------------attgctttctttt------ttgggtccaactat---gatttatagtttgattattagttttttttattgttag-gcagtagctgttgtttactgttgtacat-attctcagGCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAG
upper sequence: PP1S13_282V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ33545 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtcgtctgaaaaaccgtctcctctacttttgatggctatcttgcaaaacactgagctgaggtattgcgattccttgttggcatgctgttggttggccctatgagagtagaatcttatttctgttacttaatattatgtgtagAGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGATATGTTGAGA
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------------------------------------------------------------------------------------------gtaagttgctctctacattatgcaatgtggtttttacttccaactctc------agAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG
upper sequence: PP1S13_282V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ36895 (Selaginella moellendorffii), 3'ss of exon 6
gtaagtcgtctgaaaaaccgtctcctctacttttgatggctatcttgcaaaacactgagctgaggtattgcgattccttgttggcatgctgttggttggccctatgagagtagaatcttatttctgttacttaatattatgtgtagAGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGATATGTTGAGA
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------------------------------------------------------------------------------------------gtaagttgctctctacattatgcaatgtggtttttacttccaaccctc------agAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggttggccctatgagagtagaatcttatttctgttacttaatattatgtgtagAGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGATATGTTGAGA
acttaat putative branch site (score: 4)
aatcttatttctgtta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcgtctgaaaaaccgtctcctctacttttgatggctatcttgcaaaacactgagctgaggtattgcgattccttgttggcatgctgttggttggccctatgagagtagaatcttatttctgttacttaatattatgtgtagAGTGGAGTTCTTGCCTTGGACCCAGCTGTATTGGATACAGATCAAGTGGAAAATCTTATCAAGTTCTGCCCAACGAAGGAGGAGATGGATATGTTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA